Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marina and Zostera pacifica) beds in different geographic settings in Southern California

Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.

This is an interesting paper looking at diversity in seagrass in embayment areas, mainland open coasts, and island open coasts, and identified distinct fish communities in each location using environmental DNA (eDNA).The findings emphasize the effectiveness of eDNA analysis in characterizing local biodiversity patterns.Additionally, the study demonstrated that eDNA analysis can closely replicate visual surveys while also detecting a wider range of marine fish species.This research is significant because it compares eDNA results with in-situ surveys, which is not commonly done in the literature and highlights the importance of conducting surveys in the exact sampling areas and approximately the same time as eDNA collection.
Therefore, this study is very important and very welcome.However, some major concerns prevent me from recommending the publication of this manuscript in its current form.Below, I have specified some major and minor issues which the authors could take into consideration to improve the overall quality of the manuscript.
The introduction, discussion, and literature cited of the study primarily focus on California, which overlooks the need for a broader context and comprehensive information on previous studies conducted on environmental DNA (eDNA) in seagrass meadows.These studies are highly relevant to the current research and should be adequately incorporated into the introduction to provide a more comprehensive understanding of the subject.Some relevant studies: Introduction: The current organization of the introduction requires significant reorganization, starting with a general context to specific research gaps.Additionally, there is a notable absence of relevant literature that should be included to provide a comprehensive understanding of the topic.
Line 60 -63: Explain before how is the structural complexity of seagrass meadows (three dimensional habitatfrom belowground components with network of roots and rhizomes to aboveground components) and which components are important for fish.Also, not sure what do you mean with unstructured habitats, be more specific.Do you mean bare sand?Other macrophytes?Line 83-88: The paragraph is better placed in the earlier sections where the significance of seagrass meadows is discussed: they are are hotspots for biodiversity but have high regression rates and therefore it is necessary to monitor seagrass meadows continuously due to the changing ocean conditions and their already current regression rates.
Line 94: edna is not only used to follow biodiversity also to understand the diet of animals, trophic interactions…etc.include citation Line 97: include citation Line 104: Also include that visual census surveys are limited in scope as they tend to focus on specific taxa and are conducted at a local scale.Additionally, these surveys require taxonomic experts to accurately identify and classify organisms.Therefore, there is a potential for misidentification, which can introduce errors or uncertainties in the collected data.6: how can be that the number of species found in both surveys is bigger than the sum of edna and scuba survey? Figure 4: Fit fish species on the ordination so that their relative length indicate the correlation between species and the NMDS.

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Figure6: how can be that the number of species found in both surveys is bigger than the sum of edna and scuba survey?